Hertz used to "rent a racer" (Shelby mustang) back in the day. People would rent it, swap the engine and return it. Hertz didn't know to look for it and the hourly folks cleaning the cars didn't know what the engine should look like!
http://carguychronicles.com/2014/02/carroll-shelbys-v8-the-great-stolen-engine-caper/

I'm sure it's done now here and there swapping easy items (rims/tires, floor mats, etc) but all major items have the VIN etched in so I'm not sure how one could swap an engine/transmission/etc without getting caught. I'm shocked that's the reason they gave you. I've often said rental agencies should charge you based on a # of days, plus a set cleaning fee per rental (it costs them to clean a vehicle so why not charge more for 1 day vs 14). If you want to swap vehicles without a valid mechanic reason, you just pay an extra $10 cleaning fee and go on your way.

So did you make up a mechanical issue and swap the car the next day ("the check engine light was on this morning", "it makes a weird rattle at 60mph", etc)? 😋